scholarly journals Energy-based analysis of biomolecular pathways

Author(s):  
Peter J. Gawthrop ◽  
Edmund J. Crampin

Decomposition of biomolecular reaction networks into pathways is a powerful approach to the analysis of metabolic and signalling networks. Current approaches based on analysis of the stoichiometric matrix reveal information about steady-state mass flows (reaction rates) through the network. In this work, we show how pathway analysis of biomolecular networks can be extended using an energy-based approach to provide information about energy flows through the network. This energy-based approach is developed using the engineering-inspired bond graph methodology to represent biomolecular reaction networks. The approach is introduced using glycolysis as an exemplar; and is then applied to analyse the efficiency of free energy transduction in a biomolecular cycle model of a transporter protein [sodium-glucose transport protein 1 (SGLT1)]. The overall aim of our work is to present a framework for modelling and analysis of biomolecular reactions and processes which considers energy flows and losses as well as mass transport.

2001 ◽  
Vol 25 (9-10) ◽  
pp. 1185-1198 ◽  
Author(s):  
Sergio P. Bressa ◽  
Néstor J. Mariani ◽  
Néstor O. Ardiaca ◽  
Germán D. Mazza ◽  
Osvaldo M. Martı́nez ◽  
...  

2016 ◽  
Vol 188 ◽  
pp. 21-38 ◽  
Author(s):  
Sean T. Dix ◽  
Joseph K. Scott ◽  
Rachel B. Getman ◽  
Charles T. Campbell

Metal nanoparticles encapsulated within metal organic frameworks (MOFs) offer steric restrictions near the catalytic metal that can improve selectivity, much like in enzymes. A microkinetic model is developed for the regio-selective oxidation of n-butane to 1-butanol with O2 over a model for MOF-encapsulated bimetallic nanoparticles. The model consists of a Ag3Pd(111) surface decorated with a 2-atom-thick ring of (immobile) helium atoms which creates an artificial pore of similar size to that in common MOFs, which sterically constrains the adsorbed reaction intermediates. The kinetic parameters are based on energies calculated using density functional theory (DFT). The microkinetic model was analysed at 423 K to determine the dominant pathways and which species (adsorbed intermediates and transition states in the reaction mechanism) have energies that most sensitively affect the reaction rates to the different products, using degree-of-rate-control (DRC) analysis. This analysis revealed that activation of the C–H bond is assisted by adsorbed oxygen atoms, O*. Unfortunately, O* also abstracts H from adsorbed 1-butanol and butoxy as well, leading to butanal as the only significant product. This suggested to (1) add water to produce more OH*, thus inhibiting these undesired steps which produce OH*, and (2) eliminate most of the O2 pressure to reduce the O* coverage, thus also inhibiting these steps. Combined with increasing butane pressure, this dramatically improved the 1-butanol selectivity (from 0 to 95%) and the rate (to 2 molecules per site per s). Moreover, 40% less O2 was consumed per oxygen atom in the products. Under these conditions, a terminal H in butane is directly eliminated to the Pd site, and the resulting adsorbed butyl combines with OH* to give the desired 1-butanol. These results demonstrate that DRC analysis provides a powerful approach for optimizing catalytic process conditions, and that highly selectivity oxidation can sometimes be achieved by using a mixture of O2 and H2O as the oxidant. This was further demonstrated by DRC analysis of a second microkinetic model based on a related but hypothetical catalyst, where the activation energies for two of the steps were modified.


2021 ◽  
Vol 4 (s1) ◽  
Author(s):  
Paolo Milazzo ◽  
Roberta Gori ◽  
Alessio Micheli ◽  
Lucia Nasti ◽  
Marco Podda

We present in silico modeling methods for the investigation of dynamical properties of biochemical pathways, that are chemical reaction networks underlying cell functioning. Since pathways are (complex) dynamical systems, in-silico models are often studied by applying numerical integration techniques for Ordinary Differential Equations (ODEs), or stochastic simulation algorithms. However, these techniques require a rather accurate knowledge of the kinetic parameters of the modeled chemical reactions. Moreover, in the case of very complex reaction networks, in silico analysis can become unfeasible from the computational viewpoint. Consequently, in the last few years several approaches have been proposed that focus on estimating or predicting dynamical properties from the analysis of the structure of the biochemical pathway. This means that the analysis focuses more on the interaction patterns than on the kinetic parameters, and this usually makes it possible to deduce the role of each molecule and how each molecule qualitatively influences each other, by abstracting away from quantitative details about concentrations and reaction rates.


2016 ◽  
Vol 54 (8) ◽  
pp. 1658-1676 ◽  
Author(s):  
Attila Gábor ◽  
Katalin M. Hangos ◽  
Gábor Szederkényi

2016 ◽  
Vol 13 (120) ◽  
pp. 20160388 ◽  
Author(s):  
Adrien Henry ◽  
Olivier C. Martin

When relaxation towards an equilibrium or steady state is exponential at large times, one usually considers that the associated relaxation time τ , i.e. the inverse of the decay rate, is the longest characteristic time in the system. However, that need not be true, other times such as the lifetime of an infinitesimal perturbation can be much longer. In the present work, we demonstrate that this paradoxical property can arise even in quite simple systems such as a linear chain of reactions obeying mass action (MA) kinetics. By mathematical analysis of simple reaction networks, we pin-point the reason why the standard relaxation time does not provide relevant information on the potentially long transient times of typical infinitesimal perturbations. Overall, we consider four characteristic times and study their behaviour in both simple linear chains and in more complex reaction networks taken from the publicly available database ‘Biomodels’. In all these systems, whether involving MA rates, Michaelis–Menten reversible kinetics, or phenomenological laws for reaction rates, we find that the characteristic times corresponding to lifetimes of tracers and of concentration perturbations can be significantly longer than τ .


Author(s):  
Richard Oldani

It is hypothesized that due to mass-energy equivalence there exist transverse fields caused 7 by energy flows that are analogous to gravitomagnetic fields generated by mass flows. 8 Relativistically correct equations describing energy flow are derived by using the action integral of 9 a Lagrangian and assuming that the properties of energy, when described four-dimensionally with 10 time, are independent of the material system which supports them. The equations allow the 11 electromagnetic and gravitational energy flows to be compared revealing an underlying symmetry 12 of galactic structure.


Author(s):  
V. Annamalai ◽  
L.E. Murr

Economical recovery of copper metal from leach liquors has been carried out by the simple process of cementing copper onto a suitable substrate metal, such as scrap-iron, since the 16th century. The process has, however, a major drawback of consuming more iron than stoichiometrically needed by the reaction.Therefore, many research groups started looking into the process more closely. Though it is accepted that the structural characteristics of the resultant copper deposit cause changes in reaction rates for various experimental conditions, not many systems have been systematically investigated. This paper examines the deposit structures and the kinetic data, and explains the correlations between them.A simple cementation cell along with rotating discs of pure iron (99.9%) were employed in this study to obtain the kinetic results The resultant copper deposits were studied in a Hitachi Perkin-Elmer HHS-2R scanning electron microscope operated at 25kV in the secondary electron emission mode.


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